Tobin Roy Sosnick Department of and Molecular Biology

The University of Chicago Telephone: (773) 834-0657 929 East 57th Street Fax: (773) 702-0439 Chicago, Illinois 60637 [email protected]

Education 1989 Ph.D., Applied Physics, Harvard University, “Momentum Distribution of Normal and Superfluid Helium Using Inelastic Neutron Scattering” 1985 M.S., Applied Physics, Harvard University 1983 B.A., Physics, University of California, San Diego

Professional Experience 8/11-present Chair, Dept. of Biochemistry and Molecular Biology 10/13-present Fellow, Institute for Molecular Engineering 2009-12/11 Director, Institute for Biophysical Dynamics, University of Chicago 3/08-present Senior Fellow, Computation Institute, University of Chicago 3/07-present Professor, University of Chicago 3/06-present Chair, Graduate Program in Biophysical Sciences 5/98-present Institute for Biophysical Dynamics, University of Chicago, founding member 9/96-6/03-3/07 Assistant, Associate Professor, University of Chicago 1/96-6/96 Research Assistant Professor, University of Pennsylvania 1992-1995 Postdoctoral fellow with Prof. S.W. Englander, University of Pennsylvania 1991-1992 Postdoctoral fellow with Dr. C. Unkefer, Los Alamos National Lab 1988-1991 Postdoctoral fellow with Dr. J. Trewhella, Los Alamos National Lab 1984-1988 Predoctoral fellow with Prof. P. Sokol, Harvard University

Publications 1. Riback, J. A., Bowman, M. A., Zmyslowski, A. M., Knoverek, C. R., Jumper, J. M., Hinshaw, J. R., Kaye, E. B., Freed, K. F., Clark, P. L., and Sosnick, T. R. (2017) Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water, Science 358, 238- 241. 2. Riback, J. A., Katanski, C. D., Kear-Scott, J. L., Pilipenko, E. V., Rojek, A. E., Sosnick, T. R., and Drummond, D. A. (2017) Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response, Cell 168, 1028-1040 e1019. PMC5401687 3. Gates, Z. P., Baxa, M. C., Yu, W., Riback, J. A., Li, H., Roux, B., Kent, S. B., and Sosnick, T. R. (2017) Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core, Proc Natl Acad Sci U S A. PMC5338553 4. French, A. R., Sosnick, T. R., and Rock, R. S. (2017) Investigations of human myosin VI targeting using optogenetically controlled cargo loading, Proc Natl Acad Sci U S A 114, E1607- E1616. PMC5338507 5. Skinner, J. J., Wang, S., Lee, J., Ong, C., Sommese, R., Sivaramakrishnan, S., Koelmel, W., Hirschbeck, M., Schindelin, H., Kisker, C., Lorenz, K., Sosnick, T. R., and Rosner, M. R. (2017) A conserved salt bridge competition triggered by phosphorylation regulates the protein interactome, Proc. Natl. Acad. Sci. U S A. 6. Sachleben, J. R., Adhikari, A. N., Gawlak, G., Hoey, R. J., Liu, G., Joachimiak, A., Montelione, G. T., Sosnick, T. R., and Koide, S. (2017) Aromatic claw: A new fold with high aromatic content that evades structural prediction, Protein Sci 26, 208-217. PMC5275723 7. Poellmann, M. J., Sosnick, T. R., Meredith, S. C., and Lee, R. C. (2017) The Pentablock Amphiphilic Copolymer T1107 Prevents Aggregation of Denatured and Reduced Lysozyme, Macromol Biosci 17. PMC5497315

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8. Yu, W., Baxa, M. C., Gagnon, I., Freed, K. F., and Sosnick, T. R. (2016) Cooperative folding near the downhill limit determined with resolution by hydrogen exchange, Proc Natl Acad Sci U S A. PMCID 4855600 9. Virtanen, J. J., Sosnick, T. R., and Freed, K. F. (2016) Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)], J Chem Phys 145, 059903. PMC4975747 10. Basanta, B., Chan, K. K., Barth, P., King, T., Hinshaw, J. R., Sosnick, T. R., Liu, G., Everett, J., Xiao, R., Montelione, G. T., and Baker, D. (2016) Introduction of a polar core into the de novo designed protein Top7, Protein Sci. PMCID 4918430 11. Watkins, H. M., Simon, A. J., Sosnick, T. R., Lipman, E. A., Hjelm, R. P., and Plaxco, K. W. (2015) Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions, Proc Natl Acad Sci U S A 112, 6631-6636. PMCID 4450392 12. Baxa, M. C., Yu, W., Adhikari, A. N., Ge, L., Xia, Z., Zhou, R., Freed, K. F., and Sosnick, T. R. (2015) Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar, Proc Natl Acad Sci U S A 112, 8302-8307. PMCID 4500205 13. Zayner, J. P., and Sosnick, T. R. (2014) Factors that control the chemistry of the LOV domain photocycle, PLoS One 9, e87074. PMCID 3903614 14. Virtanen, J. J., Sosnick, T. R., and Freed, K. F. (2014) Ionic strength independence of charge distributions in solvation of biomolecules, J Chem Phys 141, 22D503. PMCID 4169388 15. Skinner, J. J., Yu, W., Gichana, E. K., Baxa, M. C., Hinshaw, J. R., Freed, K. F., and Sosnick, T. R. (2014) Benchmarking all-atom simulations using hydrogen exchange, Proc Natl Acad Sci U S A 111, 15975-15980. PMCID 4234613 16. Baxa, M. C., Haddadian, E. J., Jumper, J. M., Freed, K. F., and Sosnick, T. R. (2014) Loss of conformational in calculated using realistic ensembles and its implications for NMR-based calculations, Proc Natl Acad Sci U S A 111, 15396-15401. PMCID 4217416 17. Zayner, J. P., Antoniou, C., French, A. R., Hause, R. J., Jr., and Sosnick, T. R. (2013) Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein, Biophys J 105, 1027-1036. PMCID 3752136 18. Walters, B. T., Mayne, L., Hinshaw, J. R., Sosnick, T. R., and Englander, S. W. (2013) Folding of a large protein at high structural resolution, Proc Natl Acad Sci U S A 110, 18898-18903. PMCID 3839771 19. Sosnick, T. R., and Baxa, M. C. (2013) Revealing what gets buried first in protein folding, Proc Natl Acad Sci U S A 110, 16704-16705. PMCID 3801029 20. Sanchez-Rodriguez, J. E., Khalili-Araghi, F., Adhikari, A., Sosnick, T., Roux, B., Holmgren, M., and Bezanilla, F. (2013) Probing Conformational Changes of the Na+/K+ ATPase upon Ouabain Binding by using a Spectroscopic Approach, Biophys. J. 104, 300A-300A. 21. Parisien, M., Wang, X., Perdrizet, G., 2nd, Lamphear, C., Fierke, C. A., Maheshwari, K. C., Wilde, M. J., Sosnick, T. R., and Pan, T. (2013) Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface, Cell Rep 3, 1703-1713. PMCID 3769137 22. Liu, Y., Haddadian, E., Sosnick, T. R., Freed, K. F., and Gong, H. (2013) A Novel Implicit Solvent Model for Simulating the of RNA, Biophys. J. 105, 1248-1257. PMCID 3762369 23. Adhikari, A. N., Freed, K. F., and Sosnick, T. R. (2013) Simplified protein models: predicting folding pathways and structure using amino acid sequences, Phys Rev Lett 111, 028103. PMCID 4047675 24. Zayner, J. P., Antoniou, C., and Sosnick, T. R. (2012) The Amino-Terminal Helix Modulates Light-Activated Conformational Changes in AsLOV2, J. Mol. Biol. 419, 61-74. PMCID: PMC3338903

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25. Yoo, T. Y., Meisburger, S. P., Hinshaw, J., Pollack, L., Haran, G., Sosnick, T. R., and Plaxco, K. (2012) Small-angle X-ray scattering and single-molecule FRET produce highly divergent views of the low-denaturant unfolded state, J. Mol. Biol. 418, 226-236. PMCID 3523729 26. Yoo, T. Y., Adhikari, A., Xia, Z., Huynh, T., Freed, K. F., Zhou, R., and Sosnick, T. R. (2012) The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized), J. Mol. Biol. 420, 220-234. PMCID 3372659 27. Strickland, D., Lin, Y., Wagner, E., Hope, C. M., Zayner, J., Antoniou, C., Sosnick, T. R., Weiss, E. L., and Glotzer, M. (2012) TULIPs: tunable, light-controlled interacting protein tags for cell biology, Nature Meth. 9, 379-384. PMCID: PMC3444151 28. Shandiz, A. T., Baxa, M. C., and Sosnick, T. R. (2012) A "Link-Psi" strategy using crosslinking indicates that the folding transition state of is not very malleable, Prot. Sci. 21, 819-827. PMCID: PMC3403417 29. Perdrizet, G. A., 2nd, Artsimovitch, I., Furman, R., Sosnick, T. R., and Pan, T. (2012) Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, Proc. Natl. Acad. Sci. U S A 109, 3323-3328. PMCID: PMC3295289 30. Parisien, M., Freed, K. F., and Sosnick, T. R. (2012) On docking, scoring and assessing protein- DNA complexes in a rigid-body framework, PLoS One 7, e32647. PMCID: PMC3290582 31. DeBartolo, J., Jha, A., Freed, K. F., and Sosnick, T. R. (2012) Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States, In Protein and Peptide Folding, Misfolding, and Non-Folding, pp 79-98, John Wiley & Sons, Inc. 32. Baxa, M. C., Haddadian, E. J., Jha, A. K., Freed, K. F., and Sosnick, T. R. (2012) Context and Force Field Dependence of the Loss of Protein Back-bone Entropy upon Folding Using Realistic Denatured and Ensembles., J. Am. Chem. Soc. 134, 15929-15936. PMCID: PMC3464005 33. Adhikari, A. N., Peng, J., Wilde, M., Xu, J., Freed, K. F., and Sosnick, T. R. (2012) Modeling large regions in proteins: Applications to loops, termini, and folding, Protein Sci. 21, 107-121. PMCID 3323786 34. Adhikari, A., Freed, K. F., and Sosnick, T. R. (2012) De novo prediction of protein folding pathways and structure using the principle of sequential stabilization, Proc. Natl. Acad. Sci. U S A 109, 17442-17447. PMCID 3491489 35. Virtanen, J. J., Makowski, L., Sosnick, T. R., and Freed, K. F. (2011) Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering, Biophys. J. 101, 2061-2069. PMCID: PMC3192974 36. Sosnick, T. R., and Woodson, S. A. (2011) New era of molecular structure and dynamics from solution scattering experiments, Biopolymers 95, 503-504. PMID: 21618464 37. Sosnick, T. R., and Hinshaw, J. R. (2011) How proteins fold, Science 334, 464-465. PMID: 22034424 38. Sosnick, T. R., and Barrick, D. (2011) The folding of single domain proteins--have we reached a consensus?, Curr. Opin. Struct. Biol. 21, 12-24. PMCID: PMC3039110 39. Ralat, L. A., Kalas, V., Zheng, Z., Goldman, R. D., Sosnick, T. R., and Tang, W. J. (2011) Ubiquitin is a novel substrate for human insulin-degrading enzyme, J Mol. Biol. 406, 454-466. PMCID: PMC3064465 40. Haddadian, E. J., Gong, H., Jha, A. K., Yang, X., Debartolo, J., Hinshaw, J. R., Rice, P. A., Sosnick, T. R., and Freed, K. F. (2011) Automated real-space refinement of protein structures using a realistic backbone move set, Biophys. J. 101, 899-909. PMCID: PMC3175057 41. Zheng, Z., and Sosnick, T. R. (2010) Protein vivisection reveals elusive intermediates in folding, J. Mol. Biol. 397, 777-788. PMCID: PMC2838964

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42. Zhao, F., Peng, J., Debartolo, J., Freed, K. F., Sosnick, T. R., and Xu, J. (2010) A probabilistic and continuous model of protein conformational space for template-free modeling, J. Comp. Biol. 17, 783-798. PMCID: PMC3203516 43. Virtanen, J. J., Makowski, L., Sosnick, T. R., and Freed, K. F. (2010) Modeling the hydration layer around proteins: HyPred, Biophys. J. 99, 1611-1619. PMCID: PMC2931753 44. Strickland, D., Yao, X., Gawlak, G., Rosen, M. K., Gardner, K. H., and Sosnick, T. R. (2010) Rationally improving LOV domain-based photoswitches, Nature Meth. 7, 623-626. PMCID: PMC2914111 45. DeBartolo, J., Hocky, G., Wilde, M., Xu, J., Freed, K. F., and Sosnick, T. R. (2010) Protein structure prediction enhanced with evolutionary diversity: SPEED, Protein Sci. 19, 520-534. PMCID 2866277 46. Baird, N. J., Ludtke, S. J., Khan, H., Chiu, W., Pan, T., and Sosnick, T. R. (2010) Discrete Structure of an RNA Folding Intermediate Revealed by Cryo-electron Microscopy, J. Am. Chem. Soc. 132, 16352-16353. PMCID: PMC2988076 47. Baird, N. J., Gong, H., Zaheer, S. S., Freed, K. F., Pan, T., and Sosnick, T. R. (2010) Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion, J Mol. Biol. 397, 1298-1306. PMCID: PMC2873146 48. Zhao, F., Peng, J., Debartolo, J., Freed, K. F., Sosnick, T. R., and Xu, J. (2009) A Probabilistic Graphical Model for Ab Initio Folding, Lect Notes Comput Sci 5541, 59-73. PMCID: PMC3203516 49. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H. M., Jones, D., Brenner, S. E., Burley, S. K., Das, R., Dokholyan, N. V., Dunbrack, R. L., Jr., Fidelis, K., Fiser, A., Godzik, A., Huang, Y. J., Humblet, C., Jacobson, M. P., Joachimiak, A., Krystek, S. R., Jr., Kortemme, T., Kryshtafovych, A., Montelione, G. T., Moult, J., Murray, D., Sanchez, R., Sosnick, T. R., Standley, D. M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J. D., and Wilson, I. A. (2009) Outcome of a workshop on applications of protein models in biomedical research, Structure 17, 151-159. 50. Horn, J. R., Sosnick, T. R., and Kossiakoff, A. A. (2009) Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions, Proc. Natl. Acad. Sci. U S A 106, 2559-2564. PMCID: PMC2650303 51. DeBartolo, J., Colubri, A., Jha, A. K., Fitzgerald, J. E., Freed, K. F., and Sosnick, T. R. (2009) Mimicking the folding pathway to improve homology-free protein structure prediction, Proc. Natl. Acad. Sci. U S A 106, 3734-3739. PMCID 2656149 52. Bosco, G., Baxa, M., and Sosnick, T. (2009) Metal binding kinetics of bi-Histidine sites used in Psi-analysis: Evidence for high protein folding intermediates, Biochemistry 48, 2950- 2959. PMCID: PMC3313835 53. Baxa, M. C., Freed, K. F., and Sosnick, T. R. (2009) Psi-constrained simulations of protein folding transition states: implications for calculating Phi values., J. Mol. Biol. 386, 920-928. PMCID: PMC2742336 54. Strickland, D., Moffat, K., and Sosnick, T. R. (2008) Light-activated DNA binding in a designed allosteric protein, Proc. Natl. Acad. Sci. U S A 105, 10709–10714. PMCID: PMC2504796 55. Sosnick, T. R. (2008) Kinetic barriers and the role of topology in protein and RNA folding, Protein Sci. 17, 1308–1318. PMCID: PMC2492822 56. Smith, G. J., Lee, K. T., Qu, X., Xie, Z., Pesic, J., Sosnick, T. R., Pan, T., and Scherer, N. F. (2008) A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics, J. Mol. Biol. 378, 941-951. PMID: 18402978 57. Qu, X., Smith, G. J., Lee, K. T., Sosnick, T. R., Pan, T., and Scherer, N. F. (2008) Single- molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA, Proc. Natl. Acad. Sci. U S A 105, 6602-6607. PMCID: PMC2373323

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58. Chung, H. S., Shandiz, A., Sosnick, T. R., and Tokmakoff, A. (2008) Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding, Biochemistry 47, 13870-13877. PMCID: PMC3319365 59. Baxa, M., Freed, K. F., and Sosnick, T. R. (2008) Quantifying the Structural Requirements of the Folding Transition State of Protein A and Other Systems, J. Mol. Biol. 381, 1362-1381. PMCID: PMC2742318 60. Wong, T., Sosnick, T. R., and Pan, T. (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures, Proc. Natl. Acad. Sci. U S A 104, 17995- 18000. 61. Watters, A. L., Deka, P., Corrent, C., Callender, D., Varani, G., Sosnick, T., and Baker, D. (2007) The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection, Cell 128, 613-624. PMID: 17289578 62. Shandiz, A. T., Capraro, B. R., and Sosnick, T. R. (2007) Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state, Biochemistry 46, 13711-13719. 63. Pandit, A. D., Krantz, B. A., Dothager, R. S., and Sosnick, T. R. (2007) Characterizing protein folding transition states using Psi-analysis, Methods Mol. Biol. 350, 83-104. 64. Jacob, J., Dothager, R. S., Thiyagarajan, P., and Sosnick, T. R. (2007) Fully reduced ribonuclease A does not expand at high denaturant concentration or temperature, J Mol Biol 367, 609-615. 65. Fitzgerald, J. E., Jha, A. K., Sosnick, T. R., and Freed, K. F. (2007) Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors, Biochemistry 46, 669-682. 66. Fitzgerald, J. E., Jha, A. K., Colubri, A., Sosnick, T. R., and Freed, K. F. (2007) Reduced Cbeta statistical potentials can outperform all-atom potentials in decoy identification, Protein Sci. 16, 2123-2139. PMCID 2204143 67. Baird, N. J., Fang, X. W., Srividya, N., Pan, T., and Sosnick, T. R. (2007) Folding of a universal ribozyme: the ribonuclease P RNA, Q. Rev. Biophys. 40, 113-161. 68. Sosnick, T. R., Krantz, B. A., Dothager, R. S., and Baxa, M. (2006) Characterizing the Protein Folding Transition State Using psi Analysis, Chem. Rev. 106, 1862-1876. 69. Shi, Z., Chen, K., Liu, Z., Sosnick, T. R., and Kallenbach, N. R. (2006) PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV, Proteins 63, 312-321. 70. Ruczinski, I., Sosnick, T. R., and Plaxco, K. W. (2006) Methods for the accurate estimation of confidence intervals on protein folding phi-values, Protein Sci. 15, 2257-2264. 71. Pandit, A. D., Jha, A., Freed, K. F., and Sosnick, T. R. (2006) Small proteins fold through transition states with native-like topologies, J. Mol. Biol. 361, 755-770. 72. Pan, T., and Sosnick, T. (2006) RNA folding during transcription, Annu. Rev. Biophys. Biomol. Struct. 35, 161-175. 73. De Los Rios, M. A., Muralidhara, B. K., Wildes, D., Sosnick, T. R., Marqusee, S., Wittung- Stafshede, P., Plaxco, K. W., and Ruczinski, I. (2006) On the precision of experimentally determined protein folding rates and {phi}-values, Protein Sci 15, 553-563. 74. Colubri, A., Jha, A. K., Shen, M. Y., Sali, A., Berry, R. S., Sosnick, T. R., and Freed, K. F. (2006) Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations, J. Mol. Biol. 363, 835-857. 75. Baird, N. J., Srividya, N., Krasilnikov, A. S., Mondragon, A., Sosnick, T. R., and Pan, T. (2006) Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium, Rna 12, 598-606. 76. Wong, T., Sosnick, T. R., and Pan, T. (2005) Mechanistic insights on the folding of a large ribozyme during transcription, Biochemistry 44, 7535-7542. 77. Smith, G. J., Sosnick, T. R., Scherer, N. F., and Pan, T. (2005) Efficient labeling of a large RNA through oligonucleotide hybridization, Rna 11, 234-239.

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78. Pan, T., and Sosnick, T. R. (2005) Structural analysis of RNA and RNA-protein complexes by small-angle X-ray scattering., In Handbook of RNA biochemistry (R. Hartmann, A. B., A. Schon, E. Westhof, Ed.), pp 385-397, Wiley-VCH Verlag, Weinheim. 79. Maxwell, K. L., Wildes, D., Zarrine-Afsar, A., De Los Rios, M. A., Brown, A. G., Friel, C. T., Hedberg, L., Horng, J. C., Bona, D., Miller, E. J., Vallee-Belisle, A., Main, E. R., Bemporad, F., Qiu, L., Teilum, K., Vu, N. D., Edwards, A. M., Ruczinski, I., Poulsen, F. M., Kragelund, B. B., Michnick, S. W., Chiti, F., Bai, Y., Hagen, S. J., Serrano, L., Oliveberg, M., Raleigh, D. P., Wittung-Stafshede, P., Radford, S. E., Jackson, S. E., Sosnick, T. R., Marqusee, S., Davidson, A. R., and Plaxco, K. W. (2005) Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins, Protein Sci. 14, 602-616. 80. Krantz, B. A., Dothager, R. S., and Sosnick, T. R. (2005) Erratum to Discerning the structure and energy of multiple transition states in protein folding using psi-analysis, J. Mol. Biol. 347, 1103. 81. Jha, A. K., Colubri, A., Zaman, M. H., Koide, S., Sosnick, T. R., and Freed, K. F. (2005) Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library, Biochemistry 44, 9691-9702. 82. Jha, A. K., Colubri, A., Freed, K. F., and Sosnick, T. R. (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem, Proc. Natl. Acad. Sci. U S A 102, 13099- 13104. 83. Baird, N. J., Westhof, E., Qin, H., Pan, T., and Sosnick, T. R. (2005) Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding, J. Mol. Biol. 352, 712-722. 84. Xie, Z., Srividya, N., Sosnick, T. R., Pan, T., and Scherer, N. F. (2004) Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme, Proc. Natl. Acad. Sci. U S A 101, 534-539. PMCID: PMC327182 85. Sosnick, T. R., and Pan, T. (2004) Reduced and RNA folding rates, J. Mol. Biol. 342, 1359-1365. 86. Sosnick, T. R., Dothager, R. S., and Krantz, B. A. (2004) Differences in the folding transition state of ubiquitin indicated by phi and psi analyses, Proc. Natl. Acad. Sci. U S A 101, 17377- 17382. 87. Sosnick, T. R. (2004) Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein", Science 306, 411; author reply 411. 88. Meisner, W. K., and Sosnick, T. R. (2004) Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding, Proc. Natl. Acad. Sci. U S A 101, 15639-15644. 89. Meisner, W. K., and Sosnick, T. R. (2004) Fast folding of a helical protein initiated by the collision of unstructured chains, Proc. Natl. Acad. Sci. U S A 101, 13478-13482. 90. Krantz, B. A., Dothager, R. S., and Sosnick, T. R. (2004) Discerning the structure and energy of multiple transition states in protein folding using psi-analysis, J. Mol. Biol. 337, 463-475. 91. Kohn, J. E., Millett, I. S., Jacob, J., Zagrovic, B., Dillon, T. M., Cingel, N., Dothager, R. S., Seifert, S., Thiyagarajan, P., Sosnick, T. R., Hasan, M. Z., Pande, V. S., Ruczinski, I., Doniach, S., and Plaxco, K. W. (2004) Random-coil behavior and the dimensions of chemically unfolded proteins, Proc. Natl. Acad. Sci. U S A 101, 12491-12496. 92. Jacob, J., Krantz, B., Dothager, R. S., Thiyagarajan, P., and Sosnick, T. R. (2004) Early Collapse is not an Obligate Step in Protein Folding, J. Mol. Biol. 338, 369-382. 93. Zaman, M. H., Shen, M. Y., Berry, R. S., Freed, K. F., and Sosnick, T. R. (2003) Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides, J. Mol. Biol. 331, 693-711. 94. Sosnick, T. R., and Pan, T. (2003) RNA folding: models and perspectives, Curr. Opin. Struct. Biol. 13, 309-316.

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95. Fernandez, A., Shen, M. Y., Colubri, A., Sosnick, T. R., Berry, R. S., and Freed, K. F. (2003) Large-scale context in protein folding: villin headpiece, Biochemistry 42, 664-671. 96. Fang, X. W., Srividya, N., Golden, B. L., Sosnick, T. R., and Pan, T. (2003) Stepwise conversion of a mesophilic to a thermophilic ribozyme, J. Mol. Biol. 330, 177-183. 97. Zaman, M. H., Berry, R. S., and Sosnick, T. R. (2002) Entropic benefit of a cross-link in protein association, Proteins 48, 341-351. 98. Sosnick, T. R., and Pan, T. (2002) Getting hotter with RNA, Nature Struct. Biol. 9, 795-796. 99. Sosnick, T. R., Berry, R. S., Colubri, A., and Fernandez, A. (2002) Distinguishing foldable proteins from nonfolders: when and how do they differ?, Proteins 49, 15-23. 100. Shi, Z., Olson, C. A., Kallenbach, N. R., and Sosnick, T. R. (2002) D/H Amide Isotope Effect in Model alpha-Helical Peptides, J. Am. Chem. Soc. 124, 13994-13995. 101. Shi, Z., Krantz, B. A., Kallenbach, N., and Sosnick, T. R. (2002) Contribution of Hydrogen Bonding to Protein Stability Estimated from Isotope Effects, Biochemistry 41, 2120-2129. 102. Krantz, B. A., Srivastava, A. K., Nauli, S., Baker, D., Sauer, R. T., and Sosnick, T. R. (2002) Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects, Nature Struct. Biol. 9, 458-463. 103. Krantz, B. A., Mayne, L., Rumbley, J., Englander, S. W., and Sosnick, T. R. (2002) Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding, J. Mol. Biol. 324, 359-371. 104. Fernandez, A., Sosnick, T. R., and Colubri, A. (2002) Dynamics of hydrogen bond desolvation in protein folding, J. Mol. Biol. 321, 659-675. 105. Fang, X. W., Thiyagarajan, P., Sosnick, T. R., and Pan, T. (2002) The rate-limiting step in the folding of a large ribozyme without kinetic traps, Proc. Natl. Acad. Sci. U S A 99, 8518-8523. 106. Shelton, V. M., Sosnick, T. R., and Pan, T. (2001) Altering the Intermediate in the Equilibrium Folding of Unmodified Yeast tRNA(Phe) with Monovalent and Divalent Cations, Biochemistry 40, 3629-3638. 107. Qin, H., Sosnick, T. R., and Pan, T. (2001) Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA, Biochemistry 40, 11202-11210. 108. Lee, B. C., Croonquist, P. A., Sosnick, T. R., and Hoff, W. D. (2001) PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation, J. Biol. Chem. 23, 23. 109. Krantz, B. A., and Sosnick, T. R. (2001) Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil, Nature Struct. Biol. 8, 1042-1047. 110. Fang, X. W., Yang, X. J., Littrell, K., Niranjanakumari, S., Thiyagarajan, P., Fierke, C. A., Sosnick, T. R., and Pan, T. (2001) The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits, Rna 7, 233-241. 111. Fang, X. W., Golden, B. L., Littrell, K., Shelton, V., Thiyagarajan, P., Pan, T., and Sosnick, T. R. (2001) The thermodynamic origin of the stability of a thermophilic ribozyme, Proc Natl Acad Sci U S A 98, 4355-4360. 112. Sosnick, T. R., Fang, X., and Shelton, V. M. (2000) Application of to study RNA folding transitions, Methods Enzymol 317, 393-409. 113. Krantz, B. A., and Sosnick, T. R. (2000) Distinguishing between two-state and three-state models for ubiquitin folding, Biochemistry 39, 11696-11701. 114. Krantz, B. A., Moran, L. B., Kentsis, A., and Sosnick, T. R. (2000) D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding, Nature Struct. Biol. 7, 62-71. 115. Fang, X., Littrell, K., Yang, X., Henderson, S. J., Siefert, S., Thiyagarajan, P., Pan, T., and Sosnick, T. R. (2000) Mg(2+)-dependent compaction and folding of yeast tRNA(Phe) and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering., Biochemistry 39, 11107-11113.

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116. Shelton, V. M., Sosnick, T. R., and Pan, T. (1999) Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding, Biochemistry 38, 16831-16839. 117. Pan, T., Fang, X., and Sosnick, T. R. (1999) Pathway Modulation, Circular Permutation and Rapid RNA Folding Under Kinetic Control, J. Mol. Biol. 286, 721-731. 118. Pan, T., Artsimovitch, I., Fang, X., Landick, R., and Sosnick, T. R. (1999) Folding of a large ribozyme during transcription and the effect of the elongation factor NusA, Proc Natl Acad Sci U S A 96, 9545-9550. 119. Moran, L. B., Schneider, J. P., Kentsis, A., Reddy, G. A., and Sosnick, T. R. (1999) Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking, Proc Natl Acad Sci U S A 96, 10699-10704. 120. Fang, X., Pan, T., and Sosnick, T. R. (1999) Mg2+-dependent folding of a large ribozyme without kinetic traps, Nature Struct. Biol. 6, 1091-1095. 121. Fang, X., Pan, T., and Sosnick, T. R. (1999) A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme, Biochemistry 38, 16840-16846. 122. Bhattacharyya, R. P., and Sosnick, T. R. (1999) Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil, Biochemistry 38, 2601-2609. 123. Qi, P. X., Sosnick, T. R., and Englander, S. W. (1998) The burst phase in ribonuclease A folding and solvent dependence of the unfolded state, Nature Struct. Biol. 5, 882-884. 124. Kentsis, A., and Sosnick, T. R. (1998) Trifluoroethanol promotes helix formation by destabilizing backbone exposure: Desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding., Biochemistry 37, 14613-14622. 125. Englander, S. W., Sosnick, T. R., Mayne, L. C., Shtilerman, M., Qi, P. X., and Bai, Y. (1998) Fast and Slow Folding in Cytochrome C, Accts. of Chem. Res. 31, 737-744. 126. Sosnick, T. R., Shtilerman, M. D., Mayne, L., and Englander, S. W. (1997) Ultrafast signals in protein folding and the polypeptide contracted state, Proc Natl Acad Sci U S A 94, 8545-8550. 127. Safer, D., Sosnick, T. R., and Elzinga, M. (1997) Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends, Biochemistry 36, 5806-5816. 128. Pan, T., and Sosnick, T. R. (1997) Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance and catalytic activity, Nature Struct. Biol. 4, 931-938. 129. Englander, S. W., Mayne, L., Bai, Y., and Sosnick, T. R. (1997) Hydrogen exchange: the modern legacy of Linderstrom-Lang, Protein Sci. 6, 1101-1109. 130. Sosnick, T. R., Mayne, L., and Englander, S. W. (1996) Molecular collapse: the rate-limiting step in two-state cytochrome c folding, Proteins 24, 413-426. 131. Sosnick, T. R., Jackson, S., Wilk, R. M., Englander, S. W., and DeGrado, W. F. (1996) The role of helix formation in the folding of a fully alpha-helical coiled coil, Proteins 24, 427-432. 132. Sosnick, T. R., and Englander, S. W. (1996) What limits protein folding, In Dynamics and the problem of recognition in biological macromolecules (Jardetzky, O., and Lefevre, J.-F., Eds.), pp 65-71, Plenum Press, NY. 133. Englander, S. W., Sosnick, T. R., Englander, J. J., and Mayne, L. (1996) Mechanisms and uses of hydrogen exchange, Curr. Opin. Struct. Biol. 6, 18-23. 134. Unkefer, C. J., Houck, D. R., Britt, B. M., Sosnick, T. R., and Hanners, J. L. (1995) Biogenesis of pyrroloquinoline quinone from 3C-labeled tyrosine, Methods Enzymol 258, 227-235. 135. Sosnick, T. R., Mayne, L., Hiller, R., and Englander, S. W. (1995) The Barriers in Protein Folding, In Peptide and Protein Folding Workshop (DeGrado, W. F., Ed.), pp 52-80, International Business Communications, Philadelphia, PA. 136. Olah, G. A., Gray, D. M., Gray, C. W., Kergil, D. L., Sosnick, T. R., Mark, B. L., Vaughan, M. R., and Trewhella, J. (1995) Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study, J Mol Biol 249, 576-594.

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137. Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: native-state hydrogen exchange, Science 269, 192-197. 138. Sosnick, T. R., Mayne, L., Hiller, R., and Englander, S. W. (1994) The barriers in protein folding, Nature Struct. Biol. 1, 149-156. 139. Olah, G. A., Mitchell, R. D., Sosnick, T. R., Walsh, D. A., and Trewhella, J. (1993) Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide, Biochemistry 32, 3649-3657. 140. Sosnick, T. R., and Trewhella, J. (1992) Denatured states of ribonuclease A have compact dimensions and residual secondary structure, Biochemistry 31, 8329-8335. 141. Sosnick, T. R., Benjamin, D. C., Novotny, J., Seeger, P. A., and Trewhella, J. (1992) Distances between the antigen-binding sites of three murine antibody subclasses measured using neutron and X-ray scattering, Biochemistry 31, 1779-1786. 142. Thomas, J., Van Patten, S. M., Howard, P., Day, K. H., Mitchell, R. D., Sosnick, T., Trewhella, J., Walsh, D. A., and Maurer, R. A. (1991) Expression in Escherichia coli and characterization of the heat-stable inhibitor of the cAMP-dependent protein kinase, J Biol Chem 266, 10906-10911. 143. Sosnick, T. R., Snow, W. M., Silver, R. N., and Sokol, P. E. (1991) Deviations from the impulse approximation in liquid 4He: An experimental test at Q=23 A -1, Phys Rev B Condens Matter 43, 216-228. 144. Sosnick, T., Charles, S., Stubbs, G., Yau, P., Bradbury, E. M., Timmins, P., and Trewhella, J. (1991) Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies, Biophys J 60, 1178-1189. PMC1260173 145. Sokol, P. E., Silver, R. N., Sosnick, T. R., and Snow, W. M. (1991) Comment on "Final-state effects on the deep-inelastic response of liquid 4He", Phys Rev Lett 67, 524. 146. Sosnick, T. R., Snow, W. M., and Sokol, P. E. (1990) Deep-inelastic neutron scattering from liquid 4He, Phys Rev B Condens Matter 41, 11185-11202. 147. Herwig, K. W., Sokol, P. E., Sosnick, T. R., Snow, W. M., and Blasdell, R. C. (1990) Density dependence of the momentum distribution in normal liquid 4He, Phys Rev B Condens Matter 41, 103-110.

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